This overview lecture will review how genomics is transforming paradigms
in several areas of research, including biomedicine and agriculture, and
will explain how and why genomics is predicted to be as transformative
and disruptive to society as computing has been. This will be
illustrated with examples of DNA-based consumer products and services
industries and several "future shock" scenarios. The lecture will close
with a consideration of the computational needs of genomics projecting
to the future.

I will survey activity in my group geared toward effective compression of genomic data, key to its storage, communication, querying, and processing. Themes range from fundamental limits, through concrete algorithms enabling operations in the compressed domain, to the interplay between lossy compression and denoising. I will pose some open questions and speculate about potential for improvements moving forward. 

The most effective genomic data compression methods either assemble reads into contigs, or replace them with their alignment positions on a reference genome. Such methods require significant computational resources, but faster alternatives that avoid using explicit or de novo-constructed references fail to match their performance. We will introduce a new reference-free compressed representation for genomic data based on light de novo assembly of reads, where each read is represented as a node in a (compact) trie. We will show how to efficiently build such tries to compactly represent reads and demonstrate that among all methods using this representation (including all de novo assembly based methods), our method achieves the shortest possible output. We also provide a lower bound on the compression rate achievable on uniformly sampled genomic read data, which is approximated by our method well. Our method significantly improves the compression performance of available alternatives without compromising speed.

The Vital-it competence center of the SIB has taken advantage of its long experience in managing and analysing sequencing big data to participate in the design of the MPEG-G standard.  The presentation will emphasize some practical aspects of the MPEG-G format by presenting a few projects that illustrate the observations that guided our thoughts during the proposition phase of the standard.

In its 30 years of activity ISO/IEC JTC 1/SC 29/WG 11 – also known as Moving Picture Experts Group (MPEG) – has developed many generations of successful standards that have transformed the world of media from analog to digital. Standardized MPEG technologies in the areas of audio and video compression as well as systems related aspects like file and transport formats have enabled the efficient interoperability and the integration we all witness in the digital media field, and that have changed the industry. Four years ago, MPEG started to investigate the compression of the abundance of data produced by high-throughput sequencing machines. Requirements for this work were identified, and a close collaboration between MPEG and Working Group 5 (data processing and integration) of ISO TC 276 Biotechnology was established. Today, the MPEG-G standard (ISO/IEC 23092 Genomic Information Representation) is close to conclusion. The standard will offer high levels of compression, about one order of magnitude better than currently used formats. By utilizing the latest technologies to compress and transport sequencing data, the MPEG-G standard will provide new functionalities such as enforcement of privacy rules, selective encryption, and many more. Moreover, MPEG-G makes use of well-established MPEG technologies to provide interoperable streaming and selective data access such as those available today in the most advanced media and internet applications. Finally, MPEG-G has been developed following the rigorously open ISO standards developments procedure. Like several other MPEG standards, MPEG-G provides an open source reference implementation. ISO/IEC is also engaged in supporting the maintenance and further progression of the standard to guarantee the perenniality of the applications using MPEG-G technology.

The MPEG-G standard is currently the largest coordinated and international effort addressing the problems and limitations of current technologies and products towards a truly efficient and economical handling of genomic information. MPEG-G utilizes the latest technology to compress and transport sequencing data for complex use cases that are currently not supported by existing formats. Notable use cases addressed by MPEG-G include: Selective access to compressed data, Data streaming, Compressed file concatenation, Genomic studies aggregation, Enforcement of privacy rules, Selective encryption of sequencing data and metadata, Annotation and linkage of genomic segments, Interoperability with main existing technologies and legacy formats, and Incremental update of sequencing data and metadata. The presentation will introduce to the main new features introduced by MPEG-G and it will include a demonstration showing how MPEG-G enables seamless streaming of compressed genomic data among processing centers without the latency introduced by compression or processing. The demonstration will show how a genomic sequence alignment and analysis pipeline developed at Vital-IT (High Performance Computing Center of the Swiss Institute of Bioinformatics) is integrated with an MPEG-G compliant encoding and streaming module which sends packets of compressed genomics data from Switzerland (Lausanne) to a receiving device in the US (ISMB premises).